Identification of mebendazole as an ethylene signaling activator reveals a role of ethylene signaling in the regulation of lateral root angles.

The lateral root angle or gravitropic set-point angle (GSA) is an important trait for root system architecture (RSA) that determines the radial expansion of the root system. The GSA therefore plays a crucial role for the ability of plants to access nutrients and water in the soil. Only a few regulatory pathways and mechanisms that determine GSA are known. These mostly relate to auxin and cytokinin pathways. Here, we report the identification of a small molecule, mebendazole (MBZ), that modulates GSA in Arabidopsis thaliana roots and acts via the activation of ethylene signaling. MBZ directly acts on the serine/threonine protein kinase CTR1, which is a negative regulator of ethylene signaling. Our study not only shows that the ethylene signaling pathway is essential for GSA regulation but also identifies a small molecular modulator of RSA that acts downstream of ethylene receptors and that directly activates ethylene signaling.

Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (Oryza sativa L.).

Zinc (Zn) is an essential micronutrient for rice, but it is toxic at a high concentration, especially in acid soils. It is yet unknown which genes regulate Zn tolerance in rice. In the present study, a genome-wide association study (GWAS) was performed for Zn tolerance in rice at the seedling stage within a rice core collection, named Ting's core collection, which showed extensive phenotypic variations in Zn toxicity with high-density single-nucleotide polymorphisms (SNPs). A total of 7 and 19 quantitative trait loci (QTL) were detected using root elongation (RE) and relative root elongation (RRE) under high Zn toxicity, respectively. Among them, 24 QTL were novel, and qRRE15 was located in the same region where 3 QTL were reported previously. In addition, qRE4 and qRRE9 were identical. Furthermore, we found eight candidate genes that are involved in abiotic and biotic stress, immunity, cell expansion, and phosphate transport in the loci of qRRE8, qRRE9, and qRRE15. Moreover, four candidate genes, i.e., Os01g0200700, Os06g0621900, Os06g0493600, and Os06g0622700, were verified correlating to Zn tolerance in rice by quantitative real time-PCR (qRT-PCR). Taken together, these results provide significant insight into the genetic basis for Zn toxicity tolerance and tolerant germplasm for developing rice tolerance to Zn toxicity and improving rice production in Zn-contaminated soils.

Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis.

BACKGROUND: The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice. RESULTS: Genome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting's core collection constructed from 2262 Ting's collections with more than 3.8 million SNPs. Within Ting's core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance. CONCLUSIONS: The present study provided important information for further using these elite genes existing in Ting's core collection for improvement of rice Al tolerance.

Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.).

BACKGROUND: Cultivated rice (Oryza sativa L.) is one of the staple food for over half of the world's population. Thus, improvement of cultivated rice is important for the development of the world. It has been shown that abundant elite genes exist in rice landraces in previous studies. RESULTS: A genome-wide association study (GWAS) performed with EMMAX for 12 agronomic traits measured in both Guangzhou and Hangzhou was carried out using 150 accessions of Ting's core collection selected based on 48 phenotypic traits from 2262 accessions of Ting's collection, the GWAS included more than 3.8 million SNPs. Within Ting's core collection, which has a simple population structure, low relatedness, and rapid linkage disequilibrium (LD) decay, we found 32 peaks located closely to previously cloned genes such as Hd1, SD1, Ghd7, GW8, and GL7 or mapped QTL, and these loci might be natural variations in the cloned genes or QTL which influence potentially agronomic traits. Furthermore, we also detected 32 regions where new genes might be located, and some peaks of these new candidate genes such as the signal on chromosome 11 for heading days were even higher than that of Hd1. Detailed annotation of these significant loci were shown in this study. Moreover, according to the estimated LD decay distance of 100 to 350 kb on the 12 chromosomes in this study, we found 13 identical significant regions in the two locations. CONCLUSIONS: This research provided important information for further mining these elite genes within Ting's core collection and using them for rice breeding.

Association Mapping for Aluminum Tolerance in a Core Collection of Rice Landraces.

Trivalent aluminum (Al3+) has drastic effect on the rice production in acidic soils. Elite genes for aluminum (Al) tolerance might exist in rice landraces. Therefore, the purpose of this research is to mine the elite genes within rice landraces. Association mapping for Al tolerance traits [i.e., relative root elongation (RRE)] was performed by using a core collection of 150 accessions of rice landraces (i.e., Ting's rice core collection). Our results showed that the Ting's rice core collection possessed a wide-range of phenotypic variation for Al tolerance, and the index of Al tolerance (RRE) was ranged from 0.22 to 0.89. Moreover, the groups with different origins and compositions of indica and japonica rice showed different degrees of tolerance to varying levels of Al. These rice landraces were further screened with 274 simple sequence repeat markers, and association mapping was performed using a mixed linear model approach. The mapping results showed that a total of 23 significant (P < 0.05) trait-marker associations were detected for Al tolerance. Of these, three associations (13%) were identical to the quantitative trait loci reported previously, and other 20 associations were reported for the first time in this study. The proportion of phenotypic variance (R2) explained by 23 significant associations ranged from 5.03 to 20.03% for Al tolerance. We detected several elite alleles for Al tolerance based on multiple comparisons of allelic effects, which could be used to develop Al tolerant rice cultivars through marker-assisted breeding.

Association Analysis in Rice: From Application to Utilization.

Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding.